Based on a story by Louis L’Amour, an Army employee who has lived with Apaches helps an isolated woman and her son survive during a war with the Apaches.
On a desert ranch little Johnny Lowe (Lee Aaker) and his mother Angie Lowe (Geraldine Page) see Hondo (John Wayne) walking to them. He says he lost his horse and buys one from her that is not broken. He puts shoes on the horse and realizes her husband has been gone a while. He tells her that whites broke the treaty with the Apaches. He says he is part Indian and can smell her. Angie lets him sleep on the floor and learns he is the killer Hondo Lane. He says he lived with an Apache squaw who died. Hondo kisses Angie and leaves on the horse.
Apaches surround the house, and Vittorio (Michael Pate) tells Angie that she was told to go away. Johnny shoots at an Indian, and Vittorio becomes his blood brother. The Apaches leave and put on war paint.
At a small town Buffalo Baker (Ward Bond) helps Hondo remove his saddle. Hondo tells Major Sherry (Paul Fix) that B Troop is not coming back. Hondo gets in a fist fight with Ed Lowe (Leo Gordon).
Vittorio brings Johnny back to Angie.
Ed identifies Hondo’s horse as his, and Hondo says he is taking it back.
Vittorio tells Angie that Johnny needs a father.
A man Ed has hired is killed by an arrow. Hondo shoots the Apache to save Ed. When Ed picks up a gun and aims at him, Hondo shoots Ed dead. Apaches chase Hondo, and he kills a few before they capture him. Hondo insults the leader, and Vittorio arrives. Vittorio finds the photo of Johnny and frees Hondo. They arrange a knife fight that Hondo wins. Vittorio and his band take Hondo to Angie, who says he is her man.
Angie takes care of Hondo, who says Ed is dead. Hondo teaches Johnny to swim by throwing him in the river. Vittorio tells Hondo what to say to the soldiers, but Hondo refuses to lie. Angie tells Hondo that she loves him. Hondo tells Lt. McKay (Tim Irish) and Buffalo that Vittorio lets him live there. Lennie (James Arness) suspects that Hondo killed Ed, and Hondo hits him. Angie overheard. Hondo tells McKay that he is not leaving. Angie stops Hondo from telling Johnny about Ed.
Buffalo and the soldiers come back and say Vittorio was killed. Hondo directs Lennie where they are going. Apaches surround the wagons, and they battle. Hondo has Buffalo lead the escape, and they circle again amid shooting. They move again, and Hondo kills the leader, ending the battle. They head for California, where Hondo has a ranch.
This western manages to give the Apache viewpoint among the violent fighting on both sides. Truthfulness and respect for the freedom of others are the values that transcend the killing the violates them.